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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Stringtie --merge segfaults with pinfish input #273

Closed conchoecia closed 4 years ago

conchoecia commented 4 years ago

Hi Geo and friends-

I'm trying to use stringtie --merge to make a non-redundant geneset using files from multiple programs like AUGUSTUS, GeneMark-ET, pinfish, et cetera. Not sure if you're supporting using stringtie --merge this way, but it seems to be one of the few pieces of easy-to-use software that performs transcript merging.

I tried to use stringtie --merge on the output of pinfish using the latest stringtie release (v2.1.2), and it segfaults. The error is just 7688 Segmentation fault. I've uploaded the gzipped gtf in case you want to try to reproduce this.

Thank you-

pinfish_output.gtf.gz

gpertea commented 4 years ago

We looked into this issue (thank you for providing the example file) and it is now fixed in version 2.1.3 of StringTie that we just released.

conchoecia commented 4 years ago

Wonderful. Thank you, @gpertea!